Research in Computational Molecular Biology

1. Front Matter

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2. An Algorithmic Framework for Predicting Side-Effects of Drugs

   • Nir Atias, Roded Sharan

   Pages 1-14

3. SubMAP: Aligning Metabolic Pathways with Subnetwork Mappings

   • Ferhat Ay, Tamer Kahveci

   Pages 15-30

4. Admixture Aberration Analysis: Application to Mapping in Admixed Population Using Pooled DNA

   • Sivan Bercovici, Dan Geiger

   Pages 31-49

5. Pathway-Based Functional Analysis of Metagenomes

   • Sivan Bercovici, Itai Sharon, Ron Y. Pinter, Tomer Shlomi

   Pages 50-64

6. Hierarchical Generative Biclustering for MicroRNA Expression Analysis

   • José Caldas, Samuel Kaski

   Pages 65-79

7. Subnetwork State Functions Define Dysregulated Subnetworks in Cancer

   • Salim A. Chowdhury, Rod K. Nibbe, Mark R. Chance, Mehmet Koyutürk

   Pages 80-95

8. Proteome Coverage Prediction for Integrated Proteomics Datasets

   • Manfred Claassen, Ruedi Aebersold, Joachim M. Buhmann

   Pages 96-109

9. Discovering Regulatory Overlapping RNA Transcripts

   • Timothy Danford, Robin Dowell, Sudeep Agarwala, Paula Grisafi, Gerald Fink, David Gifford

   Pages 110-122

10. Alignment-Free Phylogenetic Reconstruction

    • Constantinos Daskalakis, Sebastien Roch

    Pages 123-137

11. Inference of Isoforms from Short Sequence Reads

    • Jianxing Feng, Wei Li, Tao Jiang

    Pages 138-157

12. The Clark Phase-able Sample Size Problem: Long-Range Phasing and Loss of Heterozygosity in GWAS

    • Bjarni V. Halldórsson, Derek Aguiar, Ryan Tarpine, Sorin Istrail

    Pages 158-173

13. A New Algorithm for Improving the Resolution of Cryo-EM Density Maps

    • Michael Hirsch, Bernhard Schölkopf, Michael Habeck

    Pages 174-188

14. Towards Automated Structure-Based NMR Resonance Assignment

    • Richard Jang, Xin Gao, Ming Li

    Pages 189-207

15. Gapped Spectral Dictionaries and Their Applications for Database Searches of Tandem Mass Spectra

    • Kyowon Jeong, Sangtae Kim, Nuno Bandeira, Pavel A. Pevzner

    Pages 208-232

16. naiveBayesCall: An Efficient Model-Based Base-Calling Algorithm for High-Throughput Sequencing

    • Wei-Chun Kao, Yun S. Song

    Pages 233-247

17. Extracting Between-Pathway Models from E-MAP Interactions Using Expected Graph Compression

    • David R. Kelley, Carl Kingsford

    Pages 248-262

18. Simultaneous Identification of Causal Genes and Dys-Regulated Pathways in Complex Diseases

    • Yoo-Ah Kim, Stefan Wuchty, Teresa M. Przytycka

    Pages 263-280

19. Incremental Signaling Pathway Modeling by Data Integration

    • Geoffrey Koh, David Hsu, P. S. Thiagarajan

    Pages 281-296

20. The Poisson Margin Test for Normalisation Free Significance Analysis of NGS Data

    • Adam Kowalczyk, Justin Bedo, Thomas Conway, Bryan Beresford-Smith

    Pages 297-309

This volume contains the papers presented at RECOMB 2010: the 14th Annual International Conference on Research in Computational Molecular Biology held in Lisbon, Portugal, during April 25–28, 2010. The RECOMB conference series was started in 1997 by Sorin Istrail, Pavel Pevzner, and Michael Waterman. RECOMB 2010 was hosted by INESC-ID and Instituto Superior Tecnico, or- nized by a committee chaired by Arlindo Oliveira and took place at the Int- national Fair of Lisbon Meeting Centre. This year, 36 papers were accepted for presentation out of 176 submissions. The papers presented were selected by the Program Committee (PC) assisted by a number of external reviewers. Each paper was reviewed by three members of the PC, or by external reviewers, and there was an extensive Web-based discussion over a period of two weeks, leading to the ?nal decisions. RECOMB 2010 also introduced a Highlights Track, in which six additional presentations by senior authors were chosen from papers published in 2009. The RECOMB conferenceseriesiscloselyassociatedwiththeJournalofComputational Biology, which traditionally publishes special issues devoted to presenting full versions of selected conference papers.

• biological networks
• cognition
• evolution
• gene expression
• genetics
• genome
• genomics
• genotyping
• molcular sequence analysis
• molecular evolution
• protein fingerprinting
• protein structures
• regulatory DNA
• sequencing
• systems biology
• algorithm analysis and problem complexity

• Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, USA

  Bonnie Berger

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